Container directives for conda overrides

Author: pinin4fjords

conf/arm.config

@@ -215,23 +215,31 @@ process {
     //// a) have seqera aarch64 conda builds
 
     withName: '.*:ALIGN_STAR:STAR_ALIGN_IGENOMES' {
-        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
         //conda = 'seqera::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
+
+        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' }
     }
 
     withName: 'STAR_GENOMEGENERATE_IGENOMES' {
-        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
         //conda = 'bioconda::star=2.6.1d bioconda::samtools=1.10 conda-forge::gawk=5.1.0'
+
+        conda = 'seqera::star=2.6.1d bioconda::samtools=1.21 conda-forge::gawk=5.1.0'
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/18/18b787cb710e54b55e04d8df4f5d363b3581c0f6008a908d7ab7de03275dfedb/data' : 'community.wave.seqera.io/library/star_samtools_gawk:c0246261b9d809e1' }
     }
 
     withName: 'RSEM_PREPAREREFERENCE' {
-        conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
         //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
+
+        conda = 'seqera::rsem=1.3.3 seqera::star=2.7.10a'
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
     }
 
     withName: 'RSEM_CALCULATEEXPRESSION' {
-        conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
         //conda = 'bioconda::rsem=1.3.3 bioconda::star=2.7.10a'
+
+        conda = 'seqera::rsem=1.3.3 seqera::star=2.6.1d'
+        container = { workflow.containerEngine == 'singularity' && !task.ext.singularity_pull_docker_container ? 'https://community-cr-prod.seqera.io/docker/registry/v2/blobs/sha256/eb/eb5a2993bc13825b1b2443f740248c56ce0730a29553683392ce6388b7a2afe3' : 'community.wave.seqera.io/library/rsem_star:0dc50db916f3de8f' }
     }
 
     //// b) need aarch64 conda builds